Course Overview
The Ensembl project at provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.
Intended Audience
The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users.
Keywords: Genetics, Genomics, Nucleic acids analysis
Skill level of training: Beginner
Language: English
Credential awarded: Certificate of attendance/completion
Type of training: Face-to-face
Venue of the course: Health Teaching Labs 1-2, Basement of Anatomy Building, UCT Medical School, Anzio Rd, Observatory, Cape Town, South Africa
Dates for the course: Monday 6th June 2016
Course organisers: Ben Moore, Nicola Mulder, CBIO@UCT
Participation: People who will be using or are using the Ensembl genome browser for their research, or would like to learn more about how to use the Ensembl browser.
Course Sponsors: H3ABioNet
Course objectives
  • Learn about the data types in Ensembl
  • Learn how to view data in the Ensembl browser
  • Learn how to mine Ensembl data using BioMart

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Thu, 01/01/1970
Registration for participants closes: Thu, 01/01/1970
Participant registration link:
Syllabus and Tools


  • Introduction to Ensembl: origin, goals and organization of the Ensembl project
  • Genes and Transcripts: guided tour of the most important pages of the Ensembl website
  • Data retrieval with BioMart: retrieving complex / large datasets using the data retrieval tool BioMart

Afternoon: two or three of the following modules will be covered, depending on the interest of the participants.

  • Comparative genomics: gene trees, orthologues and paralogues, whole genome alignments and syntenic regions
  • Variation: sequence variants, structural variants, Variant Effect Predictor
  • Regulation: annotation of regulatory elements using data from ENCODE, Roadmap Epigenomics and BLUEPRINT projects.
  • Custom annotation: uploading / attaching your own data (BED, GFF, BAM, VCF files) to Ensembl
  • Advanced access: other ways to access Ensembl data (MySQL, Perl API, REST API)

Participants should complete the application form to attend the workshop. Participants should have a general knowledge of molecular biology / genomics and a familiarity with web browsers. As there is no workshop fees, participants must take care of their own catering needs.

Course limitations
For more information, please visit
Training material availability

Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.